Due to colouring properties, synthetic organic dyes are omnipresent in many application areas, from the textile, tannery, and cosmetic to the food industries. Among them, some compounds are pharmacologically active dyes (PADs) used against selected pathogenic bacteria, fungi, and parasites. However, some of the PADs also have toxicological properties; therefore, their usage in human and veterinary medicine is restricted. The large-scale production of PADs and widespread applications have caused these dyes to permeate the aquatic environment. Despite few reports confirming PADs occurrence in bottom sediment, wild fish, and water, they are still underestimated as emerging contaminants of the water bodies. Moreover, PADs as synthetic organic dyes are stable to light and resistant to microbial treatment; hence, their decolourisation and degradation are difficult in wastewater treatment plants (WWTPs). Up to now, PADs have been found in various types of municipal and industrial wastewater. Due to the pharmacological activity and toxicological properties of some PADs and their confirmed occurrence in the aquatic environment, their presence in the environment should be monitored. The hazard potential of PADs should be assessed, considering individual levels of the aquatic food web with particular regard to tertiary consumers such as predatory fish and humans as top-level consumers. This review collects scientific data considering applications of PADs in human and veterinary medicine and their occurrence in different parts of the aquatic environment, aquaculture, and wastewater. Also, the toxicity of PADs on the individual level of the aquatic food web and risk assessments of selected dyes are presented.